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CHECK report for RTNduals on malbec2

This page was generated on 2018-10-17 08:29:52 -0400 (Wed, 17 Oct 2018).

Package 1292/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTNduals 1.4.4
Mauro Castro , Clarice Groeneveld
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RTNduals
Branch: RELEASE_3_7
Last Commit: 7049dec
Last Changed Date: 2018-09-03 11:56:38 -0400 (Mon, 03 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTNduals
Version: 1.4.4
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:RTNduals.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings RTNduals_1.4.4.tar.gz
StartedAt: 2018-10-16 03:28:39 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 03:30:43 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 124.0 seconds
RetCode: 0
Status:  OK 
CheckDir: RTNduals.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:RTNduals.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings RTNduals_1.4.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/RTNduals.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTNduals/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTNduals’ version ‘1.4.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RTNduals’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
mbrAssociation-methods        13.672  0.148  13.835
mbrDpiFilter-methods           5.300  0.040   5.346
mbrPriorEvidenceTable-methods  5.284  0.040   5.328
mbrBootstrap-methods           5.128  0.008   5.139
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

RTNduals.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL RTNduals
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘RTNduals’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RTNduals)

Tests output

RTNduals.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("RTNduals")
-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking TFs in the dataset...
-Preprocessing complete!

-Performing permutation analysis...
--For 2 regulons...

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-Permutation analysis complete! 

-Performing bootstrap analysis...
--For 2 regulons...

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-Bootstrap analysis complete! 

-Applying dpi filter...
-DPI filter complete! 

-Checking regulons and regulatory elements...
-Extrating inferred regulatory associations...
-Mapping network triplets between regulons...
-Assessing overlap between 2 regulons...

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-Assessing correlation between 2 regulons...


RUNIT TEST PROTOCOL -- Tue Oct 16 03:30:41 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RTNduals RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning message:
No 'dual regulon' has been observed for the input parameters. 
> 
> proc.time()
   user  system elapsed 
  9.024   0.236   9.270 

Example timings

RTNduals.Rcheck/RTNduals-Ex.timings

nameusersystemelapsed
mbrAssociation-methods13.672 0.14813.835
mbrBootstrap-methods5.1280.0085.139
mbrDpiFilter-methods5.3000.0405.346
mbrGet-methods1.1880.0001.190
mbrPermutation-methods1.6640.0241.689
mbrPlotDuals1.2840.0081.291
mbrPlotInteraction0.0320.0040.037
mbrPreprocess-methods1.2960.0001.295
mbrPriorEvidenceTable-methods5.2840.0405.328
tni2mbrPreprocess-methods0.6000.0080.610